Characterization and complete genome analysis of Klebsiella phage Kp109 with lytic activity against Klebsiella pneumoniae
In this study, isolation, microbiological and genomic characterization of bacteriophage Kp109 having the ability to infectK. pneumoniae has been shown. Phage Kp109 showed good killing efficiency and tolerance to a broad range of temperatures (4 –60 °C) and pH (3–9). Transmission electron microscopy and genomic analysis indicated that phage Kp109 belongs to the genusWebervirus and familyDrexlerviridae. Genomic analysis showed that the Kp109 has a 51,630 bp long double-stranded DNA genome with a GC content of 51.64%. The absence of known lysogenic, virulence, and antibiotic-resistant genes (ARGs) in its genome makes ...
Source: Virus Genes - January 27, 2024 Category: Genetics & Stem Cells Source Type: research
Determination of molecular epidemiologic pattern of human T-lymphotropic virus type 1 (HTLV-1) in Alborz province, Iran
AbstractHuman T-cell lymphotropic virus type 1 (HTLV-1) is linked to two debilitating diseases, adult T-cell leukemia/lymphoma (ATLL) and HTLV-1 associated myelopathy tropical spastic paraparesis (HAM/TSP), which are prevalent in various parts of the world, including the Alborz province in Iran. Understanding the prevalence and evolutionary relationships of HTLV-1 infections in these endemic areas is of utmost importance. In the realm of phylogenetic studies, long terminal repeat (LTR) region of HTLV-1 stands out as highly conserved, yet more variable compared to other gene segments. Consequently, it is the primary focus f...
Source: Virus Genes - January 25, 2024 Category: Genetics & Stem Cells Source Type: research
Shrimp classification for white spot syndrome detection through enhanced gated recurrent unit-based wild geese migration optimization algorithm
AbstractThe major dangerous viral infection for cultivated shrimps is WSSV. The virus is extremely dangerous, spreads swiftly, and may result in up to 100% mortality in 3 –10 days. The vast wrapped double stranded DNA virus known as WSSV describes a member of the Nimaviridae viral family’s species Whispovirus. It impacts a variety of crustacean hosts but predominantly marine shrimp species that are raised for commercial purposes. The entire age groups are affect ed by the virus, which leads to widespread mortality. Mesodermal and ectodermal tissues, like the lymph nodes, gills, and cuticular epithelium, represents the...
Source: Virus Genes - January 22, 2024 Category: Genetics & Stem Cells Source Type: research
Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia
In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia. (Source: Virus Genes)
Source: Virus Genes - January 20, 2024 Category: Genetics & Stem Cells Source Type: research
Comparative genomics of the Neodiprion sertifer nucleopolyhedrovirus from Turkey with the fewest ORFs among baculoviruses
AbstractThe complete genome of a European pine sawflyNeodiprion sertifer nucleopolyhedrovirus (NeseNPV-TR) was sequenced and characterized from next-generation sequencing data ofN. sertifer larva from T ürkiye. This genome was analyzed and compared to previously reported genomes of baculoviruses. The baculovirus phylogeny was reconstructed and the species identity of the NeseNPV-TR was delineated using K2P distance. The length of the genome was 82,052 bp, with a G + C content of 33.28%. It co ntained 83 putative ORFs, including 38 baculovirus core genes, three lepidopteran baculovirus core genes, and three non-conser...
Source: Virus Genes - January 19, 2024 Category: Genetics & Stem Cells Source Type: research
Two novel phages, Klebsiella phage GADU21 and Escherichia phage GADU22, from the urine samples of patients with urinary tract infection
AbstractPhages are found in a wide variety of places where bacteria exist including body fluids. The aim of the present study was to isolate phages from the urine samples of patients with urinary tract infection. The 10 urine samples were cultured to isolate bacteria and also used as phage sources against the isolated bacteria. From 10 urine samples with positive cultures, 3 phages were isolated (33%) and two of them were further studied. TheKlebsiella phage GADU21 andEscherichia phage GADU22 phages infectedKlebsiella pneumonia andEscherichia coli, respectively. Among the tested 14 species for host range analysis, theKlebs...
Source: Virus Genes - January 18, 2024 Category: Genetics & Stem Cells Source Type: research
DsRNA sequencing revealed a previously missed terminal sequence of a +ssRNA virus that infects dinoflagellate Heterocapsa circularisquama
AbstractHeterocapsa circularisquama RNA virus (HcRNAV) is the only dinoflagellate-infecting RNA virus cultured. However, only two strains of HcRNAV have been registered with complete genome sequences (strains 34 and 109 for UA and CY types, respectively). To extend the genomic information of HcRNAV, we performed full-genome sequencing of an unsequenced strain of HcRNAV (strain A8) using the fragmented and primer-ligated double-stranded RNA (dsRNA) sequencing (FLDS) method. The complete genome of HcRNAV A8 with 4457 nucleotides (nt) was successfully determined, and sequence alignment of the major capsid protein gene suggest...
Source: Virus Genes - January 10, 2024 Category: Genetics & Stem Cells Source Type: research
Molecular characterization of a novel variant of infectious bronchitis virus from field outbreaks in backyard chicken population of North East India
This study provides insight on recently emerging IBV outbreaks in NER, India, which might be causing huge economic losses to the poultry farmers in the region. (Source: Virus Genes)
Source: Virus Genes - January 7, 2024 Category: Genetics & Stem Cells Source Type: research
Virulence evaluation of Israeli Marek ’s disease virus isolates from commercial poultry using their meq gene sequence
AbstractFifty-seven Gallid alphaherpesvirus 2 (GaHV-2) isolates, collected during a 30-year period (1990 –2019) from commercial poultry flocks affected by Marek’s disease (MD), were molecularly characterised. The GaHV-2meq gene was amplified and sequenced to evaluate the virus virulence, based on the number of PPPPs within the proline-rich repeats (PRRs) of its transactivation domain. The present illustration of virus virulence evaluation on a large scale of field virus isolates by molecular analysis exemplifies the practical benefit and usefulness of the molecular marker in commercial GaVH-2 isolates. The alterna...
Source: Virus Genes - January 6, 2024 Category: Genetics & Stem Cells Source Type: research
A novel bluetongue virus serotype 2 strain isolated from a farmed Florida white-tailed deer (Odocoileus virginianus) arose from reassortment of gene segments derived from co-circulating serotypes in the Southeastern USA
This report documents the clinical findings, ancillary diagnostics, and genomic characterization of a novel reassortant bluetongue virus serotype 2 (BTV-2) strain isolated from a dead Florida farmed WTD in 2022. Our analyses support that this BTV-2 strain likely stemmed from the acquisition of genome segments from co-circulating BTV strains in Florida and Louisiana. In addition, our analyses also indicate that genetically uncharacterized BTV strains may be circulating in the Southeastern USA; however, the identity and reassortant status of these BTV strains cannot be determined based on the VP2 and VP5 genome sequences. He...
Source: Virus Genes - January 5, 2024 Category: Genetics & Stem Cells Source Type: research
Rapid detection of human adenovirus subgroup B using recombinase polymerase amplification assay
This study aimed to develop a product for rapid nucleic acid detection of HAdV B using recombinase polymerase amplification assay (RPA) and validate the performance of this method by using clinical samples. Results showed that this method achieved a lower limit of detection (LOD) of 10 copies/ μL and had no cross-reactivity with other adenovirus subgroups or respiratory pathogens. In addition to high sensitivity, it can be completed within 30 min at 40 °C. There is no need to perform nucleic acid extraction on clinical samples. Taking qPCR as the gold standard, the RPA assay possessed a high concordance (Cohen’s kapp...
Source: Virus Genes - January 4, 2024 Category: Genetics & Stem Cells Source Type: research
A virus from Aspergillus cibarius with features of alpha- and betachrysoviruses
AbstractFrom the ascomyceteAspergillus cibarius strain NW-FVA 2590, which was originally isolated from a root, associated with stem collar necrosis ofFraxinus excelsior L., a novel virus was isolated and characterized. Its genome is encoded on three monocistronic dsRNA segments ranging from 3683 bp (dsRNA 1) over 3093 (dsRNA 2) to 2902 bp (dsRNA 3), which are packed in isometric particles of around 35 nm. While the viral RdRp (P1) is encoded on segment 1, protein sequencing showed that two more structural proteins are present which are translated from dsRNA 2 (P2) and dsRNA 3 (P3) and p ossibly form the viral capsid. A...
Source: Virus Genes - December 30, 2023 Category: Genetics & Stem Cells Source Type: research
Full-length genome characterization of a novel mitovirus isolated from the root rot fungus Armillaria mellea
In this study, a new mitovirus denominated “Armillaria mellea mitovirus 1” (AmMV1) was identified in the sporophore samples ofArmillaria mellea, commonly known as honey mushroom. AmMV1 has a genome length of 4440 nucleotides and a G + C content of 48%. It encompasses a single open reading frame (ORF) that encodes an RNA-dependent RNA polymerase (RdRp). Comparison through BLASTp analysis revealed that the RdRp domain of AmMV1 shares a sequence identity ranging from 33.43% to 43.27% with RdRp domains ofDuamitovirus genus members, having the highest similarity (43.27%) to Rhizoctonia solani mitovirus 94. According to...
Source: Virus Genes - December 16, 2023 Category: Genetics & Stem Cells Source Type: research
First report of the whole-genome sequence analysis of avian rotavirus A from Japanese chickens
In this study, we report for the first time the whole-genome sequences of ARVA strains from Japanese chicken populations. The virus strains were inoculated to MA104 cells and cultured viruses were used to obtain the sequences with the MiSeq system, and genetic analysis demonstrated the genotype constellation of G19-P[30]-I11-R6-C6-M7-A16-N6-T8-E10-H8 of the Japanese chicken ARVA isolates. Phylogenetic analyses demonstrated that the VP1, VP2, VP3, VP4, VP7, NSP2, and NSP4 coding gene sequences of the Japanese strains were closer to those of Korean than the European ARVA strains, although such relationship was not clear for ...
Source: Virus Genes - December 15, 2023 Category: Genetics & Stem Cells Source Type: research
Enhancement of bactericidal effects of bacteriophage and gentamicin combination regimen against Staphylococcus aureus and Pseudomonas aeruginosa strains in a mice diabetic wound model
AbstractDiabetic patients are more susceptible to developing wound infections resulting in poor and delayed wound healing. Bacteriophages, the viruses that target-specific bacteria, can be used as an alternative to antibiotics to eliminate drug-resistant bacterial infections.Pseudomonas aeruginosa (P. aeruginosa) andStaphylococcus aureus (S. aureus) are among the most frequently identified pathogens in diabetic foot ulcers (DFUs). The aim of this study was assessment of bacteriophage and gentamicin combination effects on bacterial isolates from DFU infections. Specific bacteriophages were collected from sewage and animal f...
Source: Virus Genes - December 11, 2023 Category: Genetics & Stem Cells Source Type: research
